11e45667d4e291b3038ccda729a1cdf5bcaf004a
braney
  Mon Jul 11 15:46:54 2016 -0700
incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
defines, modify a bunch of makefiles to include kentSrc variable
pointing to top of the tree.

diff --git src/utils/raToSvmLight/makefile src/utils/raToSvmLight/makefile
index 2557fc2..be88254 100644
--- src/utils/raToSvmLight/makefile
+++ src/utils/raToSvmLight/makefile
@@ -1,20 +1,21 @@
+kentSrc = ../..
 include ../../inc/common.mk
 
 L += -lm
 MYLIBDIR = ../../lib/${MACHTYPE}
 MYLIBS =  ${MYLIBDIR}/jkweb.a
 
 O = raToSvmLight.o
 
 raToSvmLight: $O ${MYLIBS}
 	${CC} ${COPT} -o ${BINDIR}/raToSvmLight $O ${MYLIBS} $L
 	${STRIP} ${BINDIR}/raToSvmLight${EXE}
 
 test:
 	raToSvmLight in.ra name out.feature out.keys -good -fields=out.fields
 	diff expected.feature out.feature
 	diff expected.keys out.keys
 	diff expected.fields out.fields
 
 clean:
 	rm -f $O